scholarly journals A PROBABILISTIC FRAMEWORK TO IMPROVE MICRORNA TARGET PREDICTION BY INCORPORATING PROTEOMICS DATA

2009 ◽  
Vol 07 (06) ◽  
pp. 955-972 ◽  
Author(s):  
JINGJING LI ◽  
RENQIANG MIN ◽  
ANTHONY BONNER ◽  
ZHAOLEI ZHANG
Keyword(s):  
Mrna Expression ◽  
Mirna Expression ◽  
Probabilistic Model ◽  
Expression Level ◽  
Sequence Information ◽  
Protein Abundance ◽  
Underlying Assumption ◽  
Mrna Targets ◽  
Mirna Expression Level ◽  
Sequence Complementarity

Due to the difficulties in identifying microRNA (miRNA) targets experimentally in a high-throughput manner, several computational approaches have been proposed. To this date, most leading algorithms are based on sequence information alone. However, there has been limited overlap between these predictions, implying high false-positive rates, which underlines the limitation of sequence-based approaches. Considering the repressive nature of miRNAs at the mRNA translational level, here we describe a probabilistic model to make predictions by combining sequence complementarity, miRNA expression level, and protein abundance. Our underlying assumption is that, given sequence complementarity between a miRNA and its putative mRNA targets, the miRNA expression level should be high and the protein abundance of the mRNA should be low. Having identified a set of confident predictions, we then built a second probabilistic model to trace back to the mRNA expression of the confident targets to investigate the mechanisms of the miRNA-mediated post-transcriptional regulation. Our results suggest that translational repression (which has no effect on mRNA level), instead of mRNA degradation, is the dominant mechanism in miRNA regulation. This observation explained the previously observed discordant correlation between mRNA expression and protein abundance.

scholarly journals The Serum Cell-Free microRNA Expression Profile in MCTD, SLE, SSc, and RA Patients

2020 ◽  
Vol 9 (1) ◽  
pp. 161 ◽  
Author(s):  
Barbara Stypinska ◽  
Anna Wajda ◽  
Ewa Walczuk ◽  
Marzena Olesinska ◽  
Aleksandra Lewandowska ◽  
...  
Keyword(s):  
Connective Tissue ◽  
Signaling Pathway ◽  
Expression Profile ◽  
Mirna Expression ◽  
Lupus Erythematosus ◽  
Connective Tissue Diseases ◽  
Mirna Expression Profile ◽  
Expression Level ◽  
Control Group ◽  
Mirna Expression Level

Mixed connective tissue disease (MCTD) is a rare disorder characterized by symptoms that overlap two or more Autoimmune Connective Tissue Diseases (ACTDs). The aim of this study was to determine whether miRNAs participating in the TLRs signaling pathway could serve as biomarkers differentiating MCTD or other ACTD entities from a healthy control group and between groups of patients. Although the selected miRNA expression level was not significantly different between MCTD and control, we observed that miR-126 distinguishes MCTD patients from all other ACTD groups. The expression level of miRNAs was significantly higher in the serum of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) patients compared to controls. The miR-145 and -181a levels distinguished RA from other ACDT patients. miR-155 was specific for SLE patients. MiR-132, miR-143, and miR-29a distinguished RA and SLE patients from the systemic sclerosis (SSc) group. Additionally, some clinical parameters were significantly related to the miRNA expression profile in the SLE group. SLE and RA are characterized by a specific serum expression profile of the microRNAs associated with the Toll-like receptors (TLRs) signaling pathway. The analysis showed that their level distinguishes these groups from the control and from other ACTD patients. The present study did not reveal a good biomarker for MCTD patients.

scholarly journals Comprehensive analysis of the alteration of plasma miRNA expression level in mice exposed to diesel exhaust

2021 ◽  
Vol 8 (1) ◽  
pp. 1-6
Author(s):  
Ken Tachibana ◽  
Iori Kodaira ◽  
Noriko Kuroiwa ◽  
Ryo Uzuki ◽  
Yusuke Shinkai ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Diesel Exhaust ◽  
Comprehensive Analysis ◽  
Expression Level ◽  
Mirna Expression Level ◽  
Plasma Mirna

scholarly journals Identification of miRNA-eQTLs in maize mature leaf by GWAS

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Shu-Yun Chen ◽  
Mei-Hsiu Su ◽  
Karl A. Kremling ◽  
Nicholas K. Lepak ◽  
M. Cinta Romay ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Developmental Stages ◽  
Mature Leaf ◽  
Plant Genome ◽  
Expression Level ◽  
Genome Wide ◽  
Mirna Expression Level ◽  
Next Generation Sequencing Ngs

Abstract Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.

scholarly journals Highly Ordered Architecture of MicroRNA Cluster

2013 ◽  
Vol 2013 ◽  
pp. 1-4 ◽  
Author(s):  
Bing Shi ◽  
Mingxuan Zhu ◽  
Shuang Liu ◽  
Mandun Zhang
Keyword(s):  
Mirna Expression ◽  
Expression Patterns ◽  
Expression Level ◽  
Mirna Cluster ◽  
Microrna Cluster ◽  
Mirna Clusters ◽  
Mirna Expression Level ◽  
Cluster A ◽  
The Relationship

Although it is known that the placement of genes in a cluster may be critical for proper expression patterns, it remains largely unclear whether the orders of members in an miRNA cluster have biological insights. By investigating the relationship between expression and orders for miRNAs from the oncogenic miR-17-92 cluster, we observed a highly ordered architecture in this cluster. A significant correlation between miRNA expression level and its placement was revealed. More importantly, the placement of these miRNAs is associated with their dysregulation in cancer. Here, we presented the opinion that miRNA clusters are not arranged randomly but show highly ordered architectures, which may have critical roles in physiology and pathology.

scholarly journals Cytokine and Chemokine mRNA Expressions after Mycobacterium tuberculosis-Specific Antigen Stimulation in Whole Blood from Hemodialysis Patients with Latent Tuberculosis Infection

Diagnostics ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 595
Author(s):  
Ji Young Park ◽  
Sung-Bae Park ◽  
Heechul Park ◽  
Jungho Kim ◽  
Ye Na Kim ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mrna Expression ◽  
Whole Blood ◽  
Latent Tuberculosis Infection ◽  
Latent Tuberculosis ◽  
Expression Level ◽  
Mrna Expression Level ◽  
Healthy Individuals ◽  
Relative Mrna Expression ◽  
Mrna Expression Levels

There have been few reports on the kinetics of hemodialyzed (HD) patients’ immune responses in latent tuberculosis infection (LTBI). Therefore, in the present study, messenger ribonucleic acid (mRNA) expression levels of nine immune markers were analyzed to discriminate between HD patients with LTBI and healthy individuals. Nine cytokines and chemokines were screened through relative mRNA expression levels in whole blood samples after stimulation with Mycobacterium tuberculosis (MTB)-specific antigens from HD patients with LTBI (HD/LTBI), HD patients without LTBI, and healthy individuals, and results were compared with the QuantiFERON-TB Gold In-Tube (QFT-GIT) test. We confirmed that the C-C motif chemokine 11 (CCL11) mRNA expression level of the HD/LTBI group was significantly higher than the other two groups. Especially, the CCL11 mRNA expression level of the >0.7 IU/mL group in the QFT-GIT test was significantly higher than the <0.2 IU/mL group in the QFT-GIT test and the 0.2–0.7 IU/mL group in the QFT-GIT test (p = 0.0043). The present study reveals that the relative mRNA expression of CCL11 was statistically different in LTBI based on the current cut-off value (i.e., ≥0.35 IU/mL) and in the >0.7 IU/mL group. These results suggest that CCL11 mRNA expression might be an alternative biomarker for LTBI diagnosis in HD patients.

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